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Unlike the capture process, the evolving and the escape rates from the encounter state showed significant responses to the presence of the nonnative hydrophobic interactions (Figures 6B,C).
The encounter state was reached when the system evolved from an unbound state to a state with Qb>0 (usually have one native contact).
However, in the encounter state, nonnative hydrophobic interactions contribute energetically to the stability of the encounter complex and so a reduction in the evolving and escape rates were observed (Figures 6B,C).
[1] Until recently it was not possible to characterize the encounter state experimentally.
The concept of protein protein complex formation is evolving towards a view in which an encounter state is in dynamic equilibrium with the well-defined specific complex.
[18, 19] The formation of the encounter complex reduces the dimensionality of the diffusional search for the binding site that enables rapid ET. [1] It has been suggested that the population balance between the encounter state and the well-defined state depends on whether rapid ET can occur in encounter-state orientations.
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We define the encounter states and identified the spatial and orientational aspects.
Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states.
These deviations show that the observed PRE rates cannot be explained well on the basis of the native binding mode of HPr alone, and provide at least qualitative evidence for the existence of lowly populated encounter states in rapid exchange with the final native complex (Tang et al., 2008).
At the time of encountering state s in the future, the animal uses a factor, ψ t, related to its current internal state, to modulate the real-time motivation of the animal: r (s, ψ t ) = ψ t. r (s, ψ = 1 ).
It uses the time delay embedding theorem (DET, [2]) to display previously encountered states in a phase space.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com