Dimeric Kinesin
Created by Amelia Rode
Kinesin (PDB ID: 3KIN) is a motor protein essential in the transport of materials within cells. As a motor protein, kinesin translates the energy of ATP hydrolysis into directed movement in a cell (6). It is composed of a motor domain, where the ATP hydrolysis and energy conversion take place, and a cargo-binding domain to which the movable object is bound. The specialized structure of the kinesin allows it to be involved in several processes such as organelle, mRNA, and chromosome transport and microtubule sliding and depolymerization.
Intracellular transport via kinesins is necessary for components too large for simple diffusion. Kinesins use the ubiquitous microtubules within cells to walk cargo such as mitochondria and vesicles to various destinations. Kinesins are also essential in mitosis where they interact with spindle movement and help slide antiparallel microtubules apart into their newly forming cells. Recent research has also found that kinesins play important roles in vital mechanisms such as brain wiring, memory learning and suppression of tumorigenesis.
There are several families of kinesins and kinesin-related proteins. Kinesin-1 is the conventional, most commonly known family dealing with neuronal transport and synaptic vesicles in axons. Kinesin-5 (PDB ID: 1YRS) is another family of kinesins that has many species required for spindle separation (2). Members of this family, known as kinesin spindle proteins, form bipolar motors that pull on antiparallel microtubules (8). Another family, kinesin-13 (1V8J), consists of proteins that specialize in ATP hydrolysis and enhance the depolymerization of microtubule ends. Both of these families share amino acid sequence homology with the motor domain of kinesin-1. Mitotic centromere associated kinesin is a related protein that has implications in human gastric cancer. It is a microtubule depolymerase that is required for correct microtubule attachment during spindle formation. Expression of this kinesin-related protein was found to be much higher in cancer cells than in non-malignant cells (9).
Approximately 350 amino acids make up each motor domain of this form of kinesin. The alpha/beta secondary structure of kinesin is composed of central beta-sheets between alpha-helices within the motor head and a coiled-coil structure that makes up the neck of the motor. Kinesin has 4 chains that comprise monomers that dimerize to form the complete protein. The protein is made up of two head domains that bind ATP and microtubules and comprise the main motor activity of the molecule. These heads are connected to a long central stalk via flexible linker domains that contribute to the forward movement of the protein. The stalk domains form a coiled-coil structure and are the main factors in dimerization of the molecule. The stalks extend down to the tail domain (not shown) that binds to the material being transported (8). The kinesin heavy chains of the motor domain have a combined molecular weight of 81497.2 D and a theoretical isoelectric point of 6.12 (PDB, ExPASy).
The monomers are similar to one another with most of their differences occurring in the head-neck junction. When viewed from above, it becomes apparent that the heads of the dimer show a rotational symmetry of about 120 degrees around the coiled-coil axis. This arrangement demonstrates that the heads of the dimer cannot have equivalent interactions with the microtubules and leads us to accept the theory of a "walking" motion that allows each head a separate and distinct interaction (6).
Two types of contact occur between the two monomers. First, there is a local interaction between two loops at the end of beta strands of the different monomers. A lysine and a glutamate residue extend from the loops and fix the relative orientation of the subunits via ionic interactions caused by their opposite charges. Second, there are extensive interactions between the coiled neck helices. The protein exhibits an accumulation of residues with aliphatic chains (lysine and glutamate) that help stabilize and maintain solubility. Also, appropriate alignment of the helices leads to a juxtaposition of residues with hydrophobic side chains (leucine and isoleucine). These hydrophobic interactions tighten the dimerization of the protein.
Myosin, an actin dependent motor protein, appears to have a similar structure to kinesin. It is composed of two large heavy chains and four small light chains and a motor domain that binds to ADP for energy. Even though myosin is much larger (~850 amino acids) and the two motor proteins have virtually no sequence similarity, crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Several secondary structures overlap in the area around the nucleotide binding site (7). Despite the distinct enzyme functions and movement properties of these proteins, the structural similarity of kinesin and myosin suggests that the two motor proteins evolved from a common ancestor.
Motor proteins function through energy provided by the hydrolysis of ATP. The binding clefts have similar resiude arrangements in kinesin and mysoin, althought kinesin's cleft is much more open in comparison. In kinesin, an ADP binding site is located in each dimer head. Closer examination of the binding pocket shows that the adenine of ADP is sandwiched between His-94 and Arg-16 by stacking interactions and held in on the side by Pro-17 via hydrophobic interactions. The adenine also binds to water molecules that are associated with Pro-17 and Thr-93. The Ser-203, part of a universally conserved Ser-Ser-Arg motif and analogous to Ser-243 in myosin, interacts with the gamma-phosphate of ADP. The ribose sugar of ADP makes no direct contact with the protein (7).
When one head domain binds to a microtubule, the loss of ADP is induced and the head is strongly bonded with the microtubule. ATP binds to this leading head and causes a conformational change that swings the linker region forward to become embedded within the head domain. This movement of the linker region makes the trailing head step forward and bind the microtubule and subsequently lose its ADP. At the same time, the head that was leading and is now trailing hydrolyzes ATP to ADP and dissociates from the microtubule (8).