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.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Minehardt TJ,Cooke R,Pate E,Kollman PAdoi
10.1016/S0006-3495(01)76092-4subject
Has Abstractpub_date
2001-03-01 00:00:00pages
1151-68issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(01)76092-4journal_volume
80pub_type
杂志文章abstract：:One of the central tasks in systems biology is to understand how cells regulate their metabolism. Hierarchical regulation analysis is a powerful tool to study this regulation at the metabolic, gene-expression, and signaling levels. It has been widely applied to study steady-state regulation, but analysis of the metabo...
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journal_title：Biophysical journal
pub_type： 评论,杂志文章
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更新日期：2012-08-08 00:00:00
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更新日期：2010-10-20 00:00:00
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pub_type： 杂志文章
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更新日期：1983-04-01 00:00:00
