Folding Mechanism of Proteins Im7 and Im9: Insight from All-Atom Simulations in Implicit and Explicit Solvent.

Im7 and Im9 are evolutionary related proteins with almost identical native structures. In spite of their structural similarity, experiments show that Im7 folds through a long-lived on-pathway intermediate, while Im9 folds according to two-state kinetics. In this work, we use a recently developed enhanced path sampling method to generate many folding trajectories for these proteins, using realistic atomistic force fields, in both implicit and explicit solvent. Overall, our results are in good agreement with the experimental ϕ values and with the result of ϕ-value-restrained molecular dynamics (MD) simulations. However, our implicit solvent simulations fail to predict a qualitative difference in the folding pathways of Im7 and Im9. In contrast, our simulations in explicit solvent correctly reproduce the fact that only protein Im7 folds through a on-pathway intermediate. By analyzing our atomistic trajectories, we provide a physical picture which explains the observed difference in the folding kinetics of these chains.

Cluster phases of decorated micellar solutions with macrocyclic ligands.

An aqueous self-assembled micellar system (sodium dodecyl sulfate, SDS, decorated with various adhesive sites, cryptand Kryptofix 222 and crown ether 18-Crown-6 molecules) has been investigated by dynamic light scattering (DLS) and small angle x-ray scattering (SAXS) to have insights into the micellar structure, the micellar interactions, and the aggregation properties of the system. DLS demonstrates the existence of populations of aggregates in the submicrometer/micrometer range, while the Guinier analysis of the SAXS curves helps in detailing objects smaller than 30 nm. The aggregates of micelles are here named cluster phases of micelles (CPMs). Considering that SDS micelles in water do not aggregate at low concentration, it is shown that macrocyclic ligands induce the SDS micelle aggregation as a function of the concentration (i.e., investigated ligand/SDS molar ratios are 5.0, 1.5, 1.0, and 0.5) and hydrophobicity of the adhesive sites. The sizes and the percentages of the micelles and the CPMs have been monitored to test the stability and reversibility of the system. DLS results clearly show that the aggregation processes of the decorated micelles are reproducible at time intervals of the order of 1 month, while the stability may not be entirely maintained after a year. As an issue of particular relevance, the higher the ligand/surfactant molar ratio, the larger are the CPMs induced. The K222 ligand results in being more effective in promoting the micellar aggregation than 18C6 as a consequence of the different hydrophobicity.