5,866 research outputs found
Quantum Interactions Between Non-Perturbative Vacuum Fields
We develop an approach to investigate the non-perturbative dynamics of
quantum field theories, in which specific vacuum field fluctuations are treated
as the low-energy dynamical degrees of freedom, while all other vacuum field
configurations are explicitly integrated out from the path integral. We show
how to compute the effective interaction between the vacuum field degrees of
freedom both perturbatively (using stochastic perturbation theory) and fully
non-perturbatively (using lattice field theory simulations). The present
approach holds to all orders in the couplings and does not rely on the
semi-classical approximation.Comment: 15 pages, 4 figure
The Role of Non-native Interactions in the Folding of Knotted Proteins
Stochastic simulations of coarse-grained protein models are used to
investigate the propensity to form knots in early stages of protein folding.
The study is carried out comparatively for two homologous
carbamoyltransferases, a natively-knotted N-acetylornithine
carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase
(OTCase). In addition, two different sets of pairwise amino acid interactions
are considered: one promoting exclusively native interactions, and the other
additionally including non-native quasi-chemical and electrostatic
interactions. With the former model neither protein show a propensity to form
knots. With the additional non-native interactions, knotting propensity remains
negligible for the natively-unknotted OTCase while for AOTCase it is much
enhanced. Analysis of the trajectories suggests that the different entanglement
of the two transcarbamylases follows from the tendency of the C-terminal to
point away from (for OTCase) or approach and eventually thread (for AOTCase)
other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair
clarifies that natively-knotted proteins can spontaneously knot during early
folding stages and that non-native sequence-dependent interactions are
important for promoting and disfavoring early knotting events.Comment: Accepted for publication on PLOS Computational Biolog
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