ArticleBiophysical journal2001
Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd.
Article in Biophysical journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- Plus and minus ends of microtubules respond asymmetrically to kinesin binding by a long-range directionally driven allosteric mechanism.Science advances · 2022Article
- How Kinesin-1 Utilize the Energy of Nucleotide: The Conformational Changes and Mechanochemical Coupling in the Unidirectional Motion of Kinesin-1.International journal of molecular sciences · 2020Review
- Metal switch-controlled myosin II from Dictyostelium discoideum supports closure of nucleotide pocket during ATP binding coupled to detachment from actin filaments.The Journal of biological chemistry · 2013Article
- Mapping the structural and dynamical features of kinesin motor domains.PLoS computational biology · 2013Article
- Analysis of the interaction of the Eg5 Loop5 with the nucleotide site.Journal of theoretical biology · 2011Article
- EPR spectra and molecular dynamics agree that the nucleotide pocket of myosin V is closed and that it opens on binding actin.Journal of molecular biology · 2011Article
- A seesaw model for intermolecular gating in the kinesin motor protein.Biophysical reviews · 2011Article
- Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.Journal of molecular biology · 2011Article
- An atomic-level mechanism for activation of the kinesin molecular motors.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Analysis of the interaction of the nucleotide base with myosin and the effect on substrate efficacy.Biophysical journal · 2009Article
- The beginning of kinesin's force-generating cycle visualized at 9-A resolution.The Journal of cell biology · 2007Article
- Dynamics of the nucleotide pocket of myosin measured by spin-labeled nucleotides.Biophysical journal · 2007Article
- Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.Biophysical journal · 2005Article
- Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.Journal of computer-aided molecular design · 2005Article
- Molecular dynamics analysis of structural factors influencing back door pi release in myosin.Biophysical journal · 2004Article
- A comparative study of motor-protein motions by using a simple elastic-network model.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- A kinesin switch I arginine to lysine mutation rescues microtubule function.The Journal of biological chemistry · 2003Article
- EPR spectroscopy shows a microtubule-dependent conformational change in the kinesin switch 1 domain.Biophysical journal · 2003Article
- A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.Biophysical journal · 2002Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of the microtubule motor, ncd, from the open conformation to the closed conformation seen in myosin. MD simulations were done of both the open and the closed conformations, with either MgADP or MgATP at the active site. All MD structures were stable at 300 K for 500 ps, implying that the open and closed conformers all represented local minima on a global free energy surface. Free energy calculations indicated that the open structure was energetically favored with MgADP at the active site, suggesting why only the open structure has been captured in crystallographic work. With MgATP, the closed and open structures had roughly equal energies. Simulated annealing MD showed the transformation from the closed phosphate-tube ncd structure to an open configuration. The MD simulations also showed that the coordination of switch 1 to the nucleotide dramatically affected the position of both the bound nucleotide and switch 2 and that a closed phosphate-tube may be necessary for catalysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.