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2) Neither the hetero-FRET methods provide any direct insight into the proposed conformational changes.
The schematic diagram at the bottom illustrates the subunit-selective labeling pattern and the proposed conformational changes that are inferred from the behavior of the resonances.
Over the course of these simulations, drug and inhibitor binding have been investigated and the coordinated movements of individual helices have been correlated with the proposed conformational changes.
The subdomains of the AcrB porter domain together with the proposed conformational changes in monomer T during the T → O transition are shown in Figure 2. The latter changes have been derived from a fullTMD simulation in which all C α atoms of the whole protein have been steered.
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Toward the C terminus of rat helix α5, Pro294 mediates a sharp kink of ∼70° that very strongly reflects the proposed conformational change between helices 12/13 in BDLP.
The arc-like rotation of the helix hairpins in SeCitS is reminiscent of the recently proposed conformational change for substrate translocation in GltPh (Crisman et al., 2009; Reyes et al., 2009; Verdon et al., 2014).
Although ligand binding has been shown to be unaffected in many systems by A8-35, it has been proposed that conformational changes and interactions may be slowed.
Consistent with these proposed large conformational changes in PFL during activation by PFL-AE, recent surface plasmon resonance studies indicate that the PFL/PFL-AE binding is slow, with the rate limited by large conformational changes.
However, more recently, it has also been proposed that conformational changes in a "gating loop" (residues 398 413) result in voltage-triggered activity due to the movement of E411, which competes with the substrate for the active site.
Seeing as Rpn11 in module 1 displays elevated rates of DUB activity compared to Rpn11 or Rpn11 Rpn8 heterodimer [ 13], we propose that conformational changes upon binding of Rpn5 or other neighbours in module 1 may be sufficient to partially alleviate repression by the C-terminus of Rpn11.
An opposing "structural toxic threshold" model proposed a conformational change above the pathogenic polyQ threshold resulting in a specific toxic conformation for expanded polyQ.
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