Banushkina PV, Krivov SV. High-resolution free energy landscape analysis of protein folding. Biochem Soc Trans. 2015; 43: 157-161.Banushkina, P.V., Krivov, S.V. (2015). High-resolution free energy landscape analysis of protein folding. Biochemical society transactions, 43, 157-161...
Very interestingly, the purely hydrophobic solids exhibit aquasi-isotropic free-energy landscape around the nanopore center,F(ξ1,ξ2). Independent umbrella sampling calculations show that for the (23, 0) electrically charged nanotubes, the probability maximum at a distance ofΩ= 0.54 nm from the...
Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign...
Surprisingly, the free energy has a "multivalley landscape": there are many local minima besides those corre- sponding to the well-known IC, NC, and C CDWs. Each of these local minima corresponds to new CDW states with three-fold rotational symmetry. Despite of different global texture, ...
In this section, we focus on the analysis of the force peak obtained via these simulations, but first we start with an analytical computation of the forces using the PB model (32, 57). According to this model, the potential energy of a sequence of N + 1 basepairs whose first basepair...
Surprisingly, the free energy has a "multivalley landscape": there are many local minima besides those corre- sponding to the well-known IC, NC, and C CDWs. Each of these local minima corresponds to new CDW states with three-fold rotational symmetry. Despite of different global texture, ...
Retroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the replication cycle. Yet, strand transfer is intrinsically iso-energetic and it is not clear how efficient integration can be achieve
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Additionally, the uncertainty of the free energy landscape as computed by a Monte Carlo bootstrap error analysis in the WHAM program by Alan Grossfield111 is shown as a range in Figs S12 and S14. Discussion Statistical potential summary. RACER, a coarse-grained RNA model, can ...
Alessandro Laio1 & Michele Vendruscolo4 The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways...