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Kinesin walks processively on microtubules in an asymmetric hand-over-hand manner with each step spanning 16 nm. We used molecular simulations to determine the fraction of a single step due to conformational changes in the neck linker, and that due to diffusion of the tethered head. Stepping is determined largely by two energy scales, one favoring neck-linker docking and the other, ε hMT-TH...
Molecular dynamics simulations and single molecule experiments are used to suggest that charged helices in the medial tail domain participate in myosin VI dimerization (Kim et al., 2010), which reinforces the mechanism that unfolding of the three helix bundle in the proximal tail serves as a lever arm extension.
The detachment kinetics from actin upon ATP binding is a key step in the reaction cycle of myosin V. We show that a network of residues, constituting the allostery wiring diagram (AWD), that trigger the rigor (R) to post-rigor (PR) transition, span key structural elements from the ATP and actin-binding regions. Several of the residues are in the 33 residue helix (H18), P loop, and switch I. Brownian...
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribozymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the Tetrahymena ribozyme. Depending on the loading rate, the number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between two and four. Force-quench refolding...
The open/closed transition in polymerases is a crucial event in DNA replication and transcription. We hypothesize that the residues that transmit the signal for the open/closed transition are also strongly conserved. To identify the dynamically relevant residues, we use an elastic network model of polymerases and probe the residue-specific response to a local perturbation. In a variety of DNA/RNA...
Multiple long molecular dynamics simulations are used to probe the oligomerization mechanism of Aβ 16-22 (KLVFFAE) peptides. The peptides, in the monomeric form, adopt either compact random-coil or extended β strand-like structures. The assembly of the low-energy oligomers, in which the peptides form antiparallel β sheets, occurs by multiple pathways with the formation...
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