dorsal/arxiv
View SchemaInternal strain regulates the nucleotide binding site of the kinesin leading head
| Authors | Changbong Hyeon, Jose N. Onuchic |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0702012 |
| URL | https://arxiv.org/abs/q-bio/0702012 |
| DOI | 10.1073/pnas.0610939104 |
| Journal | PNAS (2007) vol 104, 2175-2180 |
Abstract
In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Since the processivity of kinesin is much higher than other motor proteins, it has been speculated that there exists a mechanism for allosteric regulation between the two monomers. Recent experiments suggest that ATP binding to the leading head domain in kinesin is regulated by the rearward strain built on the neck-linker. We test this hypothesis by explicitly modeling a $C_{\alpha}$-based kinesin structure whose both motor domains are bound on the tubulin binding sites. The equilibrium structures of kinesin on the microtubule show disordered and ordered neck-linker configurations for the leading and the trailing head, respectively. The comparison of the structures between the two heads shows that several native contacts present at the nucleotide binding site in the leading head are less intact than those in the binding site of the rear head. The network of native contacts obtained from this comparison provides the internal tension propagation pathway, which leads to the disruption of the nucleotide binding site in the leading head. Also, using an argument based on polymer theory, we estimate the internal tension built on the neck-linker to be f~(12-15) pN. Both of these conclusions support the experimental hypothesis.
{
"annotation_id": "ea3fbfc5-d1a5-4909-b2ee-7137c5804364",
"date_created": "2026-03-02T18:01:35.765000Z",
"date_modified": "2026-03-02T18:01:35.765000Z",
"file_hash": "569e05eba390e06bf74f98bc016e570372f08bc86b9fae733e85def948b9ea31",
"private": false,
"record": {
"abstract": "In the presence of ATP, kinesin proceeds along the protofilament of\nmicrotubule by alternated binding of two motor domains on the tubulin binding\nsites. Since the processivity of kinesin is much higher than other motor\nproteins, it has been speculated that there exists a mechanism for allosteric\nregulation between the two monomers. Recent experiments suggest that ATP\nbinding to the leading head domain in kinesin is regulated by the rearward\nstrain built on the neck-linker. We test this hypothesis by explicitly modeling\na $C_{\\alpha}$-based kinesin structure whose both motor domains are bound on\nthe tubulin binding sites. The equilibrium structures of kinesin on the\nmicrotubule show disordered and ordered neck-linker configurations for the\nleading and the trailing head, respectively. The comparison of the structures\nbetween the two heads shows that several native contacts present at the\nnucleotide binding site in the leading head are less intact than those in the\nbinding site of the rear head. The network of native contacts obtained from\nthis comparison provides the internal tension propagation pathway, which leads\nto the disruption of the nucleotide binding site in the leading head. Also,\nusing an argument based on polymer theory, we estimate the internal tension\nbuilt on the neck-linker to be f~(12-15) pN. Both of these conclusions support\nthe experimental hypothesis.",
"arxiv_id": "q-bio/0702012",
"authors": [
"Changbong Hyeon",
"Jose N. Onuchic"
],
"categories": [
"q-bio.BM",
"physics.bio-ph"
],
"doi": "10.1073/pnas.0610939104",
"journal_ref": "PNAS (2007) vol 104, 2175-2180",
"title": "Internal strain regulates the nucleotide binding site of the kinesin leading head",
"url": "https://arxiv.org/abs/q-bio/0702012"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "1ca3a00a-4199-4175-ab01-4341fc83d57c",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}