The role of native contact topology in the folding of a TIM barrel model based on the α-subunit of tryptophan synthase (αTS) from Salmonella typhimurium (Protein Data Bank structure 1BKS) was studied using both equilibrium and kinetic simulations.
For example, the density of distinct spines in the hippocampus increases 24 h after eye-blink conditioning (Leuner et al. 2003), and in vivo imaging of spines in the whisker barrel model suggests that the change in somatotopic representation induced by whisker-trimming is associated with stabilization of a subset of new spines over a period of days (Holtmaat et al. 2006).
First, nine different β-barrel models (corresponding to domain 3, residue range 176 225 and 272 346) with architecture S = n/2 were generated as described in Reboul et al., 2012.
This resulted in β-barrel models with modest variations of radius and height, in which the β-strands are tilted by 20° from the pore axis (Murzin et al., 1994).
These nine different β-barrel models were generated with slightly varying a (3.48 ± 0.1 Å) and b (4.83 ± 0.1 Å) bond lengths, where the value of a is the distance between Cα of adjacent residues in the same β-strand and b is the distance between Cα of adjacent residues in adjacent β-strands.
For the barrel stave model, α-helical peptides arrange into a bundle and insert into the bacterial membrane creating pores.
There are mainly three models, the barrel-stave model, the toroidal pores model, and the carpet model (Chih et al. 2015), which are widely accepted to describe the membrane-active action mode.
In the β-barrel structure model, the backbone and bases of ssDNA are arranged helically on an imaginary cylinder with the hollow interior of the structure which permits the insertion of SWNT of a certain diameter.
The insertion of P/LLL is facilitated by hydrophobic interactions between trileucine side chains and lipids in the membrane core, resulting in transmembrane pores, through mechanism known as "barrel-stave" model.
Recently, based on the "barrel-stave" model and the "carpet" model, Chen et al. proposed a "membrane discrimination" model for AMPs whose sole target is the biomembrane, and the peptide specificity to eukaryotic or prokaryotic cells depends upon the compositional difference in the lipids of membranes (Chen et al., 2005; Chen et al., 2007).
Two permeation mechanisms have been proposed so far: i) the barrel-stave model in which the amphipathic peptides aggregate and insert into the lipid bilayer forming a channel-like transmembrane structure.
